Sorry guys I still would not use PDF Writer to create your PDF files from Quark.
First you need to set-up distiller, decided what kind of PDF you require. Do you want lores PDF’s that look good on the screen, but are not hires? Or do you want to hires PDF’s that have to be correct to go to print.
You can set-up distiller to watch folders as well, which is what I would do.
Then open your page in Quark and using a good print driver, make PS files (Postscript Files) into the watched folders you have set-up.
If you can't fix it in 20 call someone who can.